The Bax subfamily of Bcl2-related proteins is essential for apoptotic signal transduction by c-Jun NH(2)-terminal kinase

Targeted gene disruption studies have established that the c-Jun NH(2)-terminal kinase (JNK) signaling pathway is required for stress-induced release of mitochondrial cytochrome c and apoptosis. Here we demonstrate that activated JNK is sufficient to induce rapid cytochrome c release and apoptosis. However, activated JNK fails to cause death in cells deficient of members of the Bax subfamily of proapoptotic Bcl2-related proteins. Furthermore, exposure to stress fails to activate Bax, cause cytochrome c release, and induce death in JNK-deficient cells. These data demonstrate that proapoptotic members of the Bax protein subfamily are essential for JNK-dependent apoptosis.     

Conserved codon composition of ribosomal protein coding genes in Escherichia coli,Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics

Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of limited data from related species and widely divergent sequences with no known homologs. Here, we demonstrate that codon composition, a fusion of codon usage bias and amino acid composition signals, can accurately discriminate, in the absence of sequence homology information, cytoplasmic ribosomal protein genes from all other genes of known function in Saccharomyces cerevisiae, Escherichia coli and Mycobacterium tuberculosis using an implementation of support vector machines, SVM(light). Analysis of these codon composition signals is instructive in determining features that confer individuality to ribosomal protein genes. Each of the sets of positively charged, negatively charged and small hydrophobic residues, as well as codon bias, contribute to their distinctive codon composition profile. The representation of all these signals is sensitively detected, combined and augmented by the SVMs to perform an accurate classification. Of special mention is an obvious outlier, yeast gene RPL22B, highly homologous to RPL22A but employing very different codon usage, perhaps indicating a non-ribosomal function. Finally, we propose that codon composition be used in combination with other attributes in gene/protein classification by supervised machine learning algorithms.     

Identification of Arabidopsis rat mutants

Limited knowledge currently exists regarding the roles of plant genes and proteins in the Agrobacterium tumefaciens-mediated transformation process. To understand the host contribution to transformation, we carried out root-based transformation assays to identify Arabidopsis mutants that are resistant to Agrobacterium transformation (rat mutants). To date, we have identified 126 rat mutants by screening libraries of T-DNA insertion mutants and by using various “reverse genetic” approaches. These mutants disrupt expression of genes of numerous categories, including chromatin structural and remodeling genes, and genes encoding proteins implicated in nuclear targeting, cell wall structure and metabolism, cytoskeleton structure and function, and signal transduction. Here, we present an update on the identification and characterization of these rat mutants.     

Detecting susceptibility genes in case-control studies using set association

Complex diseases are generally caused by intricate interactions of multiple genes and environmental factors. Most available linkage and association methods are developed to identify individual susceptibility genes assuming a simple disease model blind to any possible gene - gene and gene - environmental interactions. We used a set association method that uses single-nucleotide polymorphism markers to locate genetic variation responsible for complex diseases in which multiple genes are involved. Here we extended the set association method from bi-allelic to multiallelic markers. In addition, we studied the type I error rates and power for both approaches using simulations based on the coalescent process. Both bi-allelic set association (BSA) and multiallelic set association (MSA) tests have the correct type I error rates. In addition, BSA and MSA can have more power than individual marker analysis when multiple genes are involved in a complex disease. We applied the MSA approach to the simulated data sets from Genetic Analysis Workshop 13. High cholesterol level was used as the definitive phenotype for a disease. MSA failed to detect markers with significant linkage disequilibrium with genes responsible for cholesterol level. This is due to the wide spacing between the markers and the lack of association between the marker loci and the simulated phenotype.     

Endogenous assays of DNA methyltransferases: Evidence for differential activities of DNMT1, DNMT2, and DNMT3 in mammalian cells in vivo

While CpG methylation can be readily analyzed at the DNA sequence level in wild-type and mutant cells, the actual DNA (cytosine-5) methyltransferases (DNMTs) responsible for in vivo methylation on genomic DNA are less tractable. We used an antibody-based method to identify specific endogenous DNMTs (DNMT1, DNMT1b, DNMT2, DNMT3a, and DNMT3b) that stably and selectively bind to genomic DNA containing 5-aza-2'-deoxycytidine (aza-dC) in vivo. Selective binding to aza-dC-containing DNA suggests that the engaged DNMT is catalytically active in the cell. DNMT1b is a splice variant of the predominant maintenance activity DNMT1, while DNMT2 is a well-conserved protein with homologs in plants, yeast, Drosophila, humans, and mice. Despite the presence of motifs essential for transmethylation activity, catalytic activity of DNMT2 has never been reported. The data here suggest that DNMT2 is active in vivo when the endogenous genome is the target, both in human and mouse cell lines. We quantified relative global genomic activity of DNMT1, -2, -3a, and -3b in a mouse teratocarcinoma cell line. DNMT1 and -3b displayed the greatest in vivo binding avidity for aza-dC-containing genomic DNA in these cells. This study demonstrates that individual DNMTs can be tracked and that their binding to genomic DNA can be quantified in mammalian cells in vivo. The different DNMTs display a wide spectrum of genomic DNA-directed activity. The use of an antibody-based tracking method will allow specific DNMTs and their DNA targets to be recovered and analyzed in a physiological setting in chromatin.     

紫斑牡丹及其一新亚种

本文回顾了有关紫斑牡丹的调查和分类历史。它曾被混同于 P．suffruticosa,P．papaveracea 及P．suffruticosa var．papaveracea。它以叶2至3回羽状复叶,小叶17～33,花瓣白色,基部有大紫斑, 花丝黄色,花盘和柱头淡黄色区别于近缘种。种下分化为两个异域的亚种;秦岭北坡的紫斑牡丹小叶全 部或大部分分裂,是一个新亚种,P．rockii subsp．taibaishanica,而P.rockii subsp．linyanshanii T.Hong et G．L.ostii则是P．rockii subsp．rockii的多余名。     

轮钟花属的恢复及其花粉和种皮证据

光学显微镜和扫描电镜观察表明,金钱豹属(广义)花粉明显分为两个类型:Campanumoea inflata和C.javanica subsp.laponica的花粉5～8沟,外壁具相对密的短刺,刺高不过1μm,而C.lancifolia,C.celebica和C.parviflora的花粉3孔沟,外壁刺稀疏,高于2μm。种子表面纹饰也同样可分为 两类,前两个种一类,其种子表面网状,网眼规则而多角形,直径大于网脊宽度,网脊上的次级纹饰为念 珠状,而后三种为一类,其种子表面网眼不规则,直径与网脊宽度近相等,网脊上的次级纹饰绳索状。可 见花粉特征与种皮性状是高度相关的。后三个种所属的分类群就是被归并了的属Cyclocodon Griffith。 综合花粉、种皮及外部形态,这个属应予恢复。其近缘属应是Platycodon,而不是Campanumoea。     

Immunolcocalization of actin in intact and DNA—and histone—depleted nuclei and chromosomes of allium cepa

The presence of actin in eukaryotic nuclei and chromosomes,and especially in higher plant nuclei and chromosomes,has not been well established.We detected actin in meristematic cells of Allium cepa with indirect immunofluorescence technique and observed bright fluorescence in the intact nuclei and chromosomes,indicating that actin is present in the nuclei and chromosomes of the higher plant.We labeld sections of the meristematic cells of A.cepa with immunogold technique,gold parti cles were concentrated in condensed chromatin and nucleoli,confirming the results of the immunofluoresence observations.We traeated the nuclei and chromosomes of A.cepa with DNase I and 2M NaCl and obtained DNA-and histone-depleted nuclei and chromosomes.Indirect immunofluorescence tests showed that the DNA-and histonedepleted nuclei and chromosomes reacted positively with the anti-actin antibodies.These results demonstrate that the anti-actin antibodies.These results demonstrate that actin exists not only in intact nuclei and chromosomes,but also in DNA-and histone-depleted nuclei and chrmosomes of the plant.In addition,our immuno-fluorescence tests indicate that tropomyosin is present in the nuclei and chromosomes of A.cepa.     

Trichosanthin inhibits T cell activation by interfering with the recruitment of ZAP-70 to CD3 ζchain

INTRoDUCTIONThichosanthin(Tk),aplantproteinisolatedfromaChinesemedicinalherbTh-1.Correspondenceaddress:Dr.KuangYenCHoU,ShanghaiInstituteofImmunology,Shang-haiSecondMedicalUniversity28oSouthChongqingRoad,Shanghai2ooo25,China.Fax:(8621)63846383,E-mail:my@sh…     

手性环方铂络合物与DNA相互作用中的分子识别

用生物微量热技术及ＤＮＡＴｍ测量研究了手性不同的三种环方铂络合物与小牛胸腺ＤＮＡ（２００ｂｐ）作用中的特异性,发现Ｒ,Ｒ构型的与ＤＮＡ作用最强,这与癌细胞的体外筛选结果相一致．而且通过ＨＰＬＣ及１３Ｃ－ＮＭＲ研究为环方铂络合物与ＤＮＡ作用的分子机理分析找到了直接的证据．